pat's edits of screen.seqs and summary.seqs

[mothur.git] / kmerdb.cpp

diff --git a/kmerdb.cpp b/kmerdb.cpp
index 27e6997d27878577e9121e6ecfb8950cee02e0c7..9652ac472fe38e14bff9707afdaba95526c35bff 100644 (file)
--- a/kmerdb.cpp
+++ b/kmerdb.cpp
@@ -57,20 +57,19 @@ KmerDB::KmerDB(string fastaFileName, int kSize) : Database(fastaFileName), kmerS
 /**************************************************************************************************/
 
 Sequence* KmerDB::findClosestSequence(Sequence* candidateSeq){
-
-       vector<int> matches(numSeqs, 0);                                                //      a record of the sequences with shared kmers
-       vector<int> timesKmerFound(kmerLocations.size()+1, 0);  //      a record of the kmers that we have already found
+       
+       Kmer kmer(kmerSize);
        
        searchScore = 0;
        int maxSequence = 0;
-       
-       string query = candidateSeq->getUnaligned();                    //      we want to search using an unaligned dna sequence
 
-       int numKmers = query.length() - kmerSize + 1;   
-       Kmer kmer(kmerSize);
-       
+       vector<int> matches(numSeqs, 0);                                                //      a record of the sequences with shared kmers
+       vector<int> timesKmerFound(kmerLocations.size()+1, 0);  //      a record of the kmers that we have already found
+
+       int numKmers = candidateSeq->getNumBases() - kmerSize + 1;      
+
        for(int i=0;i<numKmers;i++){
-               int kmerNumber = kmer.getKmerNumber(query, i);          //      go through the query sequence and get a kmer number
+               int kmerNumber = kmer.getKmerNumber(candidateSeq->getUnaligned(), i);           //      go through the query sequence and get a kmer number
                if(timesKmerFound[kmerNumber] == 0){                            //      if we haven't seen it before...
                        for(int j=0;j<kmerLocations[kmerNumber].size();j++){//increase the count for each sequence that also has
                                matches[kmerLocations[kmerNumber][j]]++;        //      that kmer
@@ -80,14 +79,14 @@ Sequence* KmerDB::findClosestSequence(Sequence* candidateSeq){
        }
 
        for(int i=0;i<numSeqs;i++){                                                             //      find the db sequence that shares the most kmers with
-               if(matches[i] > searchScore){                                           //      the query sequence
+               if(matches[i] > searchScore){                                   //      the query sequence
                        searchScore = matches[i];
                        maxSequence = i;
                }
        }
-       searchScore = 100 * searchScore / (float)numKmers;
-       return templateSequences[maxSequence];                                  //      return the Sequence object corresponding to the db
-                                                                                                                       //      sequence with the most shared kmers.
+
+       searchScore = 100 * searchScore / (float) numKmers;             //      return the Sequence object corresponding to the db
+       return templateSequences[maxSequence];                                  //      sequence with the most shared kmers.
 }
 
 /**************************************************************************************************/